I use perlite for drainage even in my substrate mixes and have for many years. Never had an issue as I've never had a substrate eating gecko! I also use it as a hatch medium and never had a hatchling ingest it either. So I don't foresee any issues with it in the potting soil.
In any case, I cut the bamboo with many different things depending on what my project is or what the cut needs to be...all standard stuff though. I cut it to length with a chop saw. I make holes for the geckos to get in and out of the tubes with standard hole saws. And I use a dremel tool to cut the larger holes for the plants. Nothing fancy or special. I sell bamboo and custom bamboo products for vivariums, so I work with it a lot. It's a great material.